Instead of a full respec that would give all EP back in one large chunk, how about a respec system based that allowed individual skills to be untrained?
Proposal:
Let's say you thought that the Basic Kinematics skill was the best skill in the game, and you raised it to Level 10, at a cost of roughly 24,500 EP. When you realized that it wasn't as useful as you thought, you would be able to untrain levels with a high cost/penalty. The cost would be 1 million NIC per current Skill Level to go down 1 Level. The penalty would be that you would only get refunded 25% of the EP that was spent on that level.
To go from Level 10 to Level 9 in our example, it would be 10 million NIC and refund 2800 EP, out of a initial cost of 11,200 to go from 9 to 10. Total cost to go from Level 10 to Level 3 (default start for a full military character) would be 49 million NIC. The total EP that you would get back from this would be 5,964.
This would allow someone to recoup some EP from a misclick or poor skill choice, but would not be a real option to completely respec and try to follow a FOTM build.